biolockj.module.report

Class JsonReport

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.JsonReport

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class JsonReport
extends JavaModuleImpl

This BioModule is used to build a JSON file (summary.json) compiled from all OTUs in the dataset.

GUI Module Name

Json Report

Field Summary

Fields inherited from class biolockj.module.JavaModuleImpl

BLJ_OPTIONS

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
JsonReport()

Method Summary

Modifier and Type	Method and Description
protected LinkedHashMap<String,TreeSet<JsonNode>>	buildJsonMap(JsonNode rootNode) Build JsonMap from the CompileOtuCounts output directory.
List<String>	getPreRequisiteModules() Module prerequisite: CompileOtuCounts
String	getSummary() Returns summary message to be displayed by Email module so must not contain confidential info.
boolean	isValidInputModule(BioModule module) If module is a SeqModule input must contain sequence data.
protected static boolean	pipelineInputContainsOtuSummary() Check pipeline input to see if OTU summary file is the only pipeline input file.
void	runModule() Obtain parsed sample data, build root node, and create the jsonMap by passing both to buildMap().
protected LinkedHashMap<String,TreeSet<JsonNode>>	updateNodeStats(LinkedHashMap<String,TreeSet<JsonNode>> jsonMap, File stats, String level, String label) Add stats from R_CalculateStats into all of the JsonNodes.
protected String	writeNodeAndChildren(JsonNode node, boolean hasPeer, LinkedHashMap<String,TreeSet<JsonNode>> jsonMap, int nodeLevel) Build lines of text output for the Json Report file.

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getSource, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init

Constructor Detail

JsonReport

public JsonReport()

Method Detail

getPreRequisiteModules

public List<String> getPreRequisiteModules()
                                    throws Exception

Module prerequisite: CompileOtuCounts

Specified by:

getPreRequisiteModules in interface BioModule

Overrides:

getPreRequisiteModules in class BioModuleImpl

Returns:

List of BioModule Class Names

Throws:

Exception - if invalid Class names are returned as prerequisites

getSummary

public String getSummary()
                  throws Exception

Description copied from class: ScriptModuleImpl

Returns summary message to be displayed by Email module so must not contain confidential info. ModuleUtil provides summary metrics on output files

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class ScriptModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

isValidInputModule

public boolean isValidInputModule(BioModule module)

Description copied from class: JavaModuleImpl

If module is a SeqModule input must contain sequence data.

Specified by:

isValidInputModule in interface BioModule

Overrides:

isValidInputModule in class JavaModuleImpl

Parameters:

module - BioModule that ran before the current BioModule

Returns:

boolean TRUE if the previousModule output is acceptable input for the current BioModule

runModule

public void runModule()
               throws Exception

Obtain parsed sample data, build root node, and create the jsonMap by passing both to buildMap(). Set ROOT_NODE #seqs with getRootCount(jsonMap), add stats info to the jsonNodes, and finally build the JSON file.

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

buildJsonMap

protected LinkedHashMap<String,TreeSet<JsonNode>> buildJsonMap(JsonNode rootNode)
                                                        throws Exception

Build JsonMap from the CompileOtuCounts output directory.

Parameters:

rootNode - Root JsonNode is top of the hierarchy

Returns:

Map(level, Set(JsonNode)) of nodes by level

Throws:

Exception - if errors occur

updateNodeStats

protected LinkedHashMap<String,TreeSet<JsonNode>> updateNodeStats(LinkedHashMap<String,TreeSet<JsonNode>> jsonMap,
                                                                  File stats,
                                                                  String level,
                                                                  String label)
                                                           throws Exception

Add stats from R_CalculateStats into all of the JsonNodes.

Parameters:

jsonMap - LinkedHashMap(level,Set(JsonNode))

stats - Stats file

level - Config."report.taxonomyLevels"

label - Label to use in node statistics

Returns:

LinkedHashMap(level,Set(JsonNode))

Throws:

Exception - if errors occur

writeNodeAndChildren

protected String writeNodeAndChildren(JsonNode node,
                                      boolean hasPeer,
                                      LinkedHashMap<String,TreeSet<JsonNode>> jsonMap,
                                      int nodeLevel)
                               throws Exception

Build lines of text output for the Json Report file.

Parameters:

node - JsonNode is the parent node

hasPeer - boolean is true if node has peer nodes

jsonMap - LinkedHashMap(level,Set(JsonNode)) all nodes by level

nodeLevel - Config."report.taxonomyLevels"

Returns:

Json Report lines

Throws:

Exception - if errors occur

pipelineInputContainsOtuSummary

protected static boolean pipelineInputContainsOtuSummary()
                                                  throws Exception

Check pipeline input to see if OTU summary file is the only pipeline input file.

Returns:

TRUE if pipeline input

Throws:

Exception - if errors occur